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Signature symmetry class viewer app
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@gilleain
gilleain committed May 13, 2010
1 parent 2f8def0 commit e09ff2e
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Showing 5 changed files with 333 additions and 14 deletions.
70 changes: 70 additions & 0 deletions src/app/AtomSymmetryClassGenerator.java
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package app;

import java.awt.Color;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

import javax.vecmath.Point2d;

import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.renderer.RendererModel;
import org.openscience.cdk.renderer.elements.ElementGroup;
import org.openscience.cdk.renderer.elements.IRenderingElement;
import org.openscience.cdk.renderer.elements.OvalElement;
import org.openscience.cdk.renderer.generators.IAtomContainerGenerator;
import org.openscience.cdk.renderer.generators.IGeneratorParameter;
import org.openscience.cdk.signature.Orbit;

public class AtomSymmetryClassGenerator implements IAtomContainerGenerator {

private Map<Orbit, Color> orbitColorMap;

public AtomSymmetryClassGenerator() {
orbitColorMap = new HashMap<Orbit, Color>();
}

public void setOrbits(List<Orbit> orbits) {
orbitColorMap.clear();
int i = 0;
for (Orbit o : orbits) {
orbitColorMap.put(o, getColorForIndex(i));
i++;
}

}

public Color getColorForIndex(int i) {
switch (i) {
case 0: return Color.RED;
case 1: return Color.ORANGE;
case 2: return Color.YELLOW;
case 3: return Color.GREEN;
case 4: return Color.BLUE;
case 5: return Color.MAGENTA;
default: return Color.BLACK;
}
}

public IRenderingElement generate(IAtomContainer atomContainer,
RendererModel model) {
ElementGroup elements = new ElementGroup();
for (Orbit o : orbitColorMap.keySet()) {
Color color = orbitColorMap.get(o);
System.out.println("setting color " + color);
for (int i : o) {
IAtom a = atomContainer.getAtom(i);
Point2d p = a.getPoint2d();
elements.add(new OvalElement(p.x, p.y, 0.25, color));
}
}
return elements;
}

public List<IGeneratorParameter<?>> getParameters() {
return new ArrayList<IGeneratorParameter<?>>();
}

}
26 changes: 12 additions & 14 deletions src/app/MoleculePanel.java
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Expand Up @@ -19,12 +19,9 @@
import org.openscience.cdk.layout.StructureDiagramGenerator;
import org.openscience.cdk.renderer.AtomContainerRenderer;
import org.openscience.cdk.renderer.RendererModel;
import org.openscience.cdk.renderer.elements.IRenderingElement;
import org.openscience.cdk.renderer.font.AWTFontManager;
import org.openscience.cdk.renderer.generators.BasicAtomGenerator;
import org.openscience.cdk.renderer.generators.BoundsGenerator;
import org.openscience.cdk.renderer.generators.IAtomContainerGenerator;
import org.openscience.cdk.renderer.generators.IGeneratorParameter;
import org.openscience.cdk.renderer.selection.IChemObjectSelection;
import org.openscience.cdk.renderer.visitor.AWTDrawVisitor;

Expand All @@ -43,7 +40,14 @@ public class MoleculePanel extends JPanel {
private BasicAtomGenerator basicAtomGenerator;

public MoleculePanel(int panelWidth, int panelHeight) {
renderer = new AtomContainerRenderer(getGenerators(), new AWTFontManager());
this(panelWidth, panelHeight, new ArrayList<IAtomContainerGenerator>());
}

public MoleculePanel(int panelWidth, int panelHeight,
List<IAtomContainerGenerator> initialGenerators) {
initialGenerators.addAll(getGenerators());
renderer = new AtomContainerRenderer(
initialGenerators, new AWTFontManager());
setRenderingParameters();
sdg = new StructureDiagramGenerator();
this.setPreferredSize(new Dimension(panelWidth, panelHeight));
Expand Down Expand Up @@ -76,16 +80,6 @@ private void setRenderingParameters() {
private List<IAtomContainerGenerator> getGenerators() {
List<IAtomContainerGenerator> generators =
new ArrayList<IAtomContainerGenerator>();
generators.add(new IAtomContainerGenerator() {
public IRenderingElement generate(IAtomContainer ac, RendererModel m) {
return new BoundsGenerator().generate((IMolecule)ac, m);
}

public List<IGeneratorParameter<?>> getParameters() {
return new ArrayList<IGeneratorParameter<?>>();
}

});
// generators.add(new RingGenerator());
// generators.add(new BasicBondGenerator());
generators.add(new TmpBondGenerator());
Expand Down Expand Up @@ -146,6 +140,10 @@ public void setMolecule(IMolecule molecule) {
repaint();
}

public void setMoleculeWithoutLayout(IMolecule molecule) {
this.molecule = molecule;
repaint();
}

private IMolecule diagramGenerate(IMolecule molecule) {
this.sdg.setMolecule(molecule, true);
Expand Down
130 changes: 130 additions & 0 deletions src/app/SignatureClassViewer.java
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package app;

import java.awt.BorderLayout;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

import javax.swing.JFrame;
import javax.swing.event.ListSelectionEvent;
import javax.swing.event.ListSelectionListener;

import org.openscience.cdk.Molecule;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.io.ISimpleChemObjectReader;
import org.openscience.cdk.io.MDLReader;
import org.openscience.cdk.io.ReaderFactory;
import org.openscience.cdk.renderer.generators.IAtomContainerGenerator;
import org.openscience.cdk.signature.MoleculeSignature;
import org.openscience.cdk.signature.Orbit;

public class SignatureClassViewer extends JFrame implements ListSelectionListener {

private MoleculePanel moleculePanel;

private TreeThumbViewer treeThumbViewer;

private Map<String, Orbit> orbitMap;

private AtomSymmetryClassGenerator atomSymmetryClassGenerator;

public SignatureClassViewer(String[] args) {
setLayout(new BorderLayout());

List<IAtomContainerGenerator> initialGenerators =
new ArrayList<IAtomContainerGenerator>();
atomSymmetryClassGenerator = new AtomSymmetryClassGenerator();
initialGenerators.add(atomSymmetryClassGenerator);

moleculePanel = new MoleculePanel(700, 700, initialGenerators);
add(moleculePanel, BorderLayout.CENTER);

treeThumbViewer = new TreeThumbViewer(700, 700);
add(treeThumbViewer, BorderLayout.EAST);
treeThumbViewer.addSelectionListener(this);

orbitMap = new HashMap<String, Orbit>();

String filename;
if (args.length != 0) {
filename = args[0];
loadFile(filename);
}
pack();
setVisible(true);
}

public void loadFile(String filename) {
try {
ReaderFactory factory = new ReaderFactory();
ISimpleChemObjectReader reader =
new MDLReader(new FileReader(filename));
// factory.createReader(new FileReader(filename));
if (reader == null) return;
IMolecule molecule = reader.read(new Molecule());
System.out.println("read");
moleculePanel.setMoleculeWithoutLayout(molecule);
for (int i = 0; i < molecule.getAtomCount(); i++) {
List<IAtom> connected =
molecule.getConnectedAtomsList(molecule.getAtom(i));
System.out.print(connected.size() + " " + (i + 1) + " ");
for (IAtom a : connected) {
int j = molecule.getAtomNumber(a) + 1;
System.out.print(j + ",");
}
System.out.println();
}
makeSignatures(molecule);


} catch (FileNotFoundException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} catch (CDKException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}

public void makeSignatures(IMolecule molecule) {
MoleculeSignature molSig = new MoleculeSignature(molecule);
List<Orbit> orbits = molSig.calculateOrbits();
orbitMap.clear();
for (Orbit o : orbits) {
String sig = o.getLabel();
treeThumbViewer.addSignature(sig);
orbitMap.put(sig, o);
}
}

public void displaySelectedOrbits(List<Orbit> orbits) {
atomSymmetryClassGenerator.setOrbits(orbits);
repaint();
}


public static void main(String[] args) {
// new SignatureClassViewer(args);
new SignatureClassViewer(new String[] { "/Users/maclean/fullerene_28.mol"});
}

public void valueChanged(ListSelectionEvent e) {
List<String> selectedList = treeThumbViewer.getSelected();
List<Orbit> selectedOrbits = new ArrayList<Orbit>();
for (String selected : selectedList) {
System.out.println("selected " + orbitMap.get(selected));
selectedOrbits.add(orbitMap.get(selected));
}
displaySelectedOrbits(selectedOrbits);
}

}
54 changes: 54 additions & 0 deletions src/app/SignatureTreeListCellRenderer.java
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package app;

import java.awt.Color;
import java.awt.Component;
import java.awt.Dimension;
import java.awt.Graphics;

import javax.swing.JList;
import javax.swing.JPanel;
import javax.swing.ListCellRenderer;

import signature.AbstractVertexSignature;
import signature.ColoredTree;
import signature.display.DisplayableColoredTree;

public class SignatureTreeListCellRenderer extends JPanel implements
ListCellRenderer {

private String signature;

public SignatureTreeListCellRenderer(int w, int h) {
setPreferredSize(new Dimension(w, h));
}

public Component getListCellRendererComponent(JList list, Object value,
int index, boolean isSelected, boolean cellHasFocus) {
if (value instanceof String) {
signature = (String) value;
}

if (isSelected) {
setBackground(Color.RED);
setForeground(Color.WHITE);
} else {
setBackground(Color.WHITE);
setForeground(Color.BLACK);
}

return this;
}

public void paint(Graphics g) {
super.paint(g);
if (signature != null) {
int w = getWidth() - 2;
int h = getHeight() - 2;
ColoredTree tree = AbstractVertexSignature.parse(signature);
DisplayableColoredTree displayTree = new DisplayableColoredTree(w, h);
displayTree.makeFromColoredTree(tree);
displayTree.paint(g);
}
}

}
67 changes: 67 additions & 0 deletions src/app/TreeThumbViewer.java
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package app;

import java.awt.Dimension;
import java.util.ArrayList;
import java.util.List;

import javax.swing.DefaultListModel;
import javax.swing.JList;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.event.ListSelectionListener;

public class TreeThumbViewer extends JPanel {

public int numberOfPanels;

public int thumbWidth;

public int thumbHeight;

private JScrollPane scrollPane;

private JList list;

public TreeThumbViewer(int w, int h) {
numberOfPanels = 0;
thumbWidth = 300;
thumbHeight = 200;
list = new JList(new DefaultListModel());
list.setCellRenderer(new SignatureTreeListCellRenderer(
thumbWidth, thumbHeight));
scrollPane = new JScrollPane(list,
JScrollPane.VERTICAL_SCROLLBAR_ALWAYS,
JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);

add(scrollPane);
Dimension d = new Dimension(w, h);
scrollPane.setPreferredSize(d);
setPreferredSize(d);
}

public void addSelectionListener(ListSelectionListener listener) {
list.addListSelectionListener(listener);
}

public List<String> getSelected() {
List<String> selected = new ArrayList<String>();
for (Object o : list.getSelectedValues()) {
if (o instanceof String) {
selected.add((String) o);
}
}
return selected;
}

public void addSignature(String signature) {
((DefaultListModel)list.getModel()).addElement(signature);
repaint();
}

public void clear() {
((DefaultListModel)list.getModel()).clear();
repaint();
}

}

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